Tag: ATAC-seq
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How To Analyze ATAC-seq Data For Absolute Beginners Part 4: ATAC-seq and RNA-seq Integration
Introduction: The Power of Multi-omics Integration Modern genomics research has evolved beyond studying isolated molecular mechanisms. To truly understand complex biological processes and disease mechanisms, researchers need to examine multiple layers of genomic information simultaneously. This tutorial introduces beginners to the powerful approach of integrating ATAC-seq and RNA-seq data using R, enabling a more comprehensive…
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How To Analyze ATAC-seq Data For Absolute Beginners Part 3: Footprinting Analysis
Introduction: Unveiling Transcription Factor Binding Sites with ATAC-seq Footprinting After mastering the basics of ATAC-seq data processing and peak calling in our previous tutorials, we now delve into one of the most powerful analytical techniques this assay enables: footprinting analysis. While standard ATAC-seq analysis reveals regions of open chromatin, footprinting takes this a step further…
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How To Analyze ATAC-seq Data For Absolute Beginners Part 2: Differential Binding Analysis Using DiffBind
Introduction: The Power of Comparative ATAC-seq Analysis ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) has revolutionized chromatin accessibility mapping by requiring minimal input material and offering streamlined workflows. While identifying accessible regions in a single condition provides valuable insights, the most compelling biological discoveries often come from comparing accessibility between different experimental conditions –…
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How To Analyze ATAC-seq Data For Absolute Beginners Part 1: From FASTQ To Peaks
Introduction: Understanding ATAC-seq At the heart of molecular biology lies a fundamental question: how do cells regulate which genes are expressed and when? One powerful technique to explore this question is Assay for Transposase-Accessible Chromatin sequencing, commonly known as ATAC-seq. This tutorial introduces beginners to the fascinating world of ATAC-seq data analysis using HOMER and…
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Recent Posts
- The Complete Guide to NGS Data Types and Formats: From Raw Reads to Analysis-Ready Files
- How To Analyze CUT&RUN/Tag Data For Absolute Beginners: From FASTQ to Peaks
- How To Analyze ATAC-seq Data For Absolute Beginners Part 4: ATAC-seq and RNA-seq Integration
- How To Analyze ATAC-seq Data For Absolute Beginners Part 3: Footprinting Analysis
Tags
Adapter Trimming Alternative Splicing Analysis ATAC-seq BAM ChIP-seq chromatin accessibility Conda Environment Setting Count DESeq2 Differential Expression edgeR FASTQ gene expression Gene Expression Quantification HOMER HPC Isoform limma MACS2 miRNA miRNA-seq Normalization PCA peak calling R Reads Mapping RNAseq analysis RNAseq analysis for beginners RStudio Transcript